python - Biopython error - The system cannot find the file specified -

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python - Biopython error - The system cannot find the file specified -

i have encountered error not able resolve.

i trying perform easiest set of commands perform tblastn algorithm, looking sequence (sequence specified "pytanie.fasta" file) in database (also specified file -> cucumber.fasta). result saved in "wynik.txt" file.

the code looks following:

from bio.blast. applications import ncbitblastncommandline database = r"\biopython\cucumber.fasta" qr = r"\biopython\pytanie.fasta" output = r"\biopython\wynik.txt" e = raw_input("enter e-value: ") tblastn_cline = ncbitblastncommandline(cmd='blastn', db=database, query=qr, out=output, evalue=e, outfmt=7) print tblastn_cline stdout, stderr = tblastn_cline()

and error get:

file "c:\users\ibm_admin\desktop\python\workspace\biopython\blast.py", line 20, in <module> stdout, stderr = tblastn_cline() file "c:\python27\lib\site-packages\bio\application\__init__.py", line 435, in __call__ shell=(sys.platform!="win32")) file "c:\python27\lib\subprocess.py", line 679, in __init__ errread, errwrite) file "c:\python27\lib\subprocess.py", line 893, in _execute_child startupinfo) windowserror: [error 2] scheme cannot find file specified

i using:

eclipse sdk version: 3.7.1 python version 2.7 os: 64 bit windows 7

i have tried on 32-bit windows xp , produces same error. biopython bundle should work fine since went through tests suggested biopython website. have tried other formats of path files located, did not work. friend uses same code on ubuntu , works fine.

does know how prepare error?

what paths of files?

the path r"\biopython\cucumber.fasta", example, absolute path on current drive (because starts backslash , no drive letter), think in case r"c:\biopython\cucumber.fasta". correct?

python eclipse pydev biopython

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